adding testing data from OWID reading fn

NEWS

@@ -1,5 +1,6 @@
 Jan 2021: More data sources added _ ver 2.1
 		- Vaccination data, from OWID
+		- Testing data, from OWID
 		- pandemics data, from Visual Capitalist infographics
 		- report.Tor fn, to report overview analysis of Toronto data
 

R/covid19_vaccination_testing.R

@@ -1,42 +1,52 @@
-# functions to obtain covid19 vaccination data
-# SRC: Our World In Data
+# functions to obtain covid19 Vaccination & Testing data
+# SRC: "Our World In Data" (OWID)
 #
 # M.Ponce - covid19.analytics 
 
 
 OWID.repos <- function(tgt) {
 #' function to define the OWID repos URLs
 #'
-#' @param  tgt  target case:  'global','us','country','locations'
+#' @param  tgt  target case:  'VAC.global','VAC.us','VAC.country','VAC.locations', 'testing'
 #'
 #' @return  URL
 #'
 
 	# OWID gtihub repo
-	owid.repo <- "https://raw.githubusercontent.com/owid/covid-19-data/master/public/data/vaccinations/"
-	vacc.locns <- paste0(owid.repo,"locations.csv")
+	#owid.repo <- "https://raw.githubusercontent.com/owid/covid-19-data/master/public/data/vaccinations/"
+	owid.repo <- "https://raw.githubusercontent.com/owid/covid-19-data/master/public/data/"
+	vacc.repo <- paste0(owid.repo,"vaccinations/")
+	vacc.locns <- paste0(vacc.repo,"locations.csv")
+	testing.repo <-  paste0(owid.repo,"testing/")
+	testing.data <- paste0(testing.repo, "covid-testing-all-observations.csv")
+	testing.data.details <- paste0(testing.repo,"covid-testing-latest-data-source-details.csv")
 
 	# United States vaccination data
 	#
 	# State-by-state data on United States COVID-19 vaccinations. We rely on the data updated daily by the United States Centers for Disease Control and Prevention. Stored in us_state_vaccinations.csv.
-	vacc.us <- paste0(owid.repo,"us_state_vaccinations.csv")
+	vacc.us <- paste0(vacc.repo,"us_state_vaccinations.csv")
 
 	# Vaccination data
 	#
 	# Country-by-country data on global COVID-19 vaccinations. We only rely on figures that are verifiable based on public official sources. Stored in vaccinations.csv.
-	vacc.global <- paste0(owid.repo,"vaccinations.csv")
+	vacc.global <- paste0(vacc.repo,"vaccinations.csv")
 
 	# specific per country -- it will be one file per country
-	vacc.country <- paste0(owid.repo,"country_data/")
+	vacc.country <- paste0(vacc.repo,"country_data/")
 
-	if (tgt == 'locations') {
+	# VACINATION REPOS
+	if (tgt == 'VAC.locations') {
 		repo <- vacc.locns
-	} else if (tgt == 'us') {
+	} else if (tgt == 'VAC.us') {
 		repo <- vacc.us
-	} else if (tgt == 'global') {
+	} else if (tgt == 'VAC.global') {
 		repo <- vacc.global
-	} else if (tgt == 'country') {
+	} else if (tgt == 'VAC.country') {
 		repo <- vacc.country
+	# TESTING REPOS
+	} else if (tgt == 'testing') {
+		repo <- testing.data
+	# UNRECOGNIZED option
 	} else {
 		stop("Error : unrecognized target! -- ",tgt)
 	}
@@ -45,11 +55,14 @@ OWID.repos <- function(tgt) {
 }
 
 
-c19.vaccination <- function(repo, disclaimer=TRUE){
-#' function to read data from OWID repo
+c19.OWID.data <- function(repo, disclaimer=TRUE){
+#' function to read data from OWID repos
 #'
 #' @param  repo  URL for reading the data
 #' @param  disclaimer  indicate whether the information about the source of the data is disclosed 
+#'
+#' @return  datafram object
+#'
 
 	vacc.data <- read.csv(repo)
 
@@ -68,14 +81,17 @@ covid19.vaccination <- function(tgt="global", data.fmt='orig', disclaimer=TRUE){
 #' @param  tgt  selects data type: 'global','us','country','locations'
 #' @param  data.fmt  selects the format of the data, options are: 'orig' (original as reported by the OWID repo)
 #' @param  disclaimer  indicates whether the information about the source of the data is disclosed
+#'
+#' @export
 #'
 
 	# select repo depending on target
+	tgt <- paste0("VAC.",tgt)
 	repo <- OWID.repos(tgt)
 
 	# distinguish between 'country' and everything else
 	if (tgt != 'country') {
-		return(c19.vaccination(repo,disclaimer))
+		return(c19.OWID.data(repo,disclaimer))
 	} else {
 		skip <- c("European Union","World")
 		# obtain list of countries
@@ -88,8 +104,28 @@ covid19.vaccination <- function(tgt="global", data.fmt='orig', disclaimer=TRUE){
 		for (cty in ctries) {
 			# convert names into URL notation, ie. spaces -> %20
 			cty <- gsub("[[:space:]]", "%20", cty)
-			vacc.countries[[cty]] <- c19.vaccination(paste0(repo,"/",cty,'.csv'))
+			vacc.countries[[cty]] <- c19.OWID.data(paste0(repo,"/",cty,'.csv'))
 		}
 		return(vacc.countries)
 	}
 }
+
+
+
+covid19.testing.data <- function(disclaimer=TRUE){
+#' function to read data related to covid19 Testing from OWID repo
+#'
+#' @param  disclaimer  indicates whether the information about the source of the data is disclosed
+#'
+#' @return  dataframe containing list of countries (Entity) and testing data
+#'
+#' @export
+#'
+
+	tgt <- "testing"
+	repo <- OWID.repos("testing")
+
+	tst.data <- c19.OWID.data(repo,disclaimer)
+
+	return(tst.data)
+}